Truth or lies?
by DarkAngelChemical
Summary: Ianto comes home to find a woman dead in his living room, he know who she is, but he doesn't tell the team. The team soon learn who she is and how Ianto knew her.
1. Chapter 1

**Truth or lies?**

**Summary: Ianto comes home to find a woman dead in his living room, he knows who she is but, he doesn't tell anyone. The team soon learn who she really is and how Ianto knew her. **

As the car rolled into the driveway of Ianto house, Ianto got a strange feeling that someone was in the house, 'Ianto?' Jack questioned, he must of seen worry on Ianto's face.

"Wait here." Ianto ordered Jack, as he climbed out the car, while pulling out his gun. Jack then watched Ianto move stealthily up the driveway and into the house. Jack had never seen Ianto move like that before, it was more like army or marine movement not Torchwood, and he wondered where he learnt to move like that.

Ianto opened the first door which led to the kitchen, nothing seemed out of the ordinary, so he turned and headed straight into the living room. Ianto stopped dead, almost dropping his gun in shock; he stared at the young woman, his half sister lying in her own pool of blood. He walked towards her and dropped it a squat position to examine the body by not touching it. Ianto noticed her knuckles were grazed; she had obviously put up a fight.

'Ianto, what happened?" Jack asked from the doorway, almost making Ianto jump.

"I don't know, I just found her like this." Ianto said quietly. He stood up to face Jack.

"Do you know who she is?" Jack asked, looking back and forth between the woman and Ianto.

"No." Ianto lied smoothly.

**Sorry for the very shorts chapter, I hoped you liked it, do you want me to continue. Please review **


	2. Chapter 2

**Truth or lies?**

Chapter 2 

"We are going to search your whole house for anything that could help us learn how that woman got into your house and how she ended up dead." Owen explained to Ianto smoothly. Ianto, Jack, Tosh, Owen and Gwen were all sitting at the table in the boardroom, starting the investigation.

"Jack." Gwen started, looking up from the photos of body to look at Jack, "why are we investigating this, shouldn't we pass this along to the police? I mean, there is nothing alien about this, the woman was shot, by the looks of it she fought for her life as if a man attacked her not some sort of alien."

"Gwen has a point Jack." Tosh said joining the conversation.

Jack, who was sitting at the head of the table, he looked at his team and answered "because Ianto works for Torchwood, and if he has any connection with this it then involves me as his boss." He then looked directly at Ianto and said in a stern voice "as it is your house is the crime scene you cannot be a part of this investigation, do you understand? Also it's for your own safety." Ianto didn't verbally reply he just nodded his understanding instead. "Owen, have you worked out who she is yet?" Jack asked, his tone slightly changing.

Owen sighed, "that's the problem it's going to be hard to identify her, she has no fingerprints, by the looks of it, they have been erased."

"Erased?" Jack repeated, he didn't take in what Owen just said.

"Yes Jack erased, she doesn't have any." Owen said simply.

"It is possible to have your fingerprints removed to avoid identification, but it's a bit pointless because you can use teeth and search through dental records." Ianto explained quietly.

"How did you know that?" Tosh asked, slightly surprised that Ianto would know this, she didn't even know this.

"It's kind of common sense." He said, giving a small shrug.

"I did take some scrapings from her teeth and Tosh is running that through the database now." Owen informed Jack.

"Okay, we have nothing more to talk to about, Tosh come to me as soon as you have a name, Owen come to me when you find out more about how she died. Ianto I want to talk to you in my office." Jack ordered as he watched everyone get up and leave. When Jack got up Ianto followed him down to his office, shutting the office door as soon as they were both in.

"Ianto, I want you to take at least two weeks off." Jack said simply. He was leaning perched on the front of his desk, facing Ianto, who was standing directly in front of him.

"Why?" Ianto asked quickly.

"It's an order don't question it." Jack growled, "Your leave starts from now, I don't care where you go or what you do, just don't be in or near the Hub for two weeks, understood?"

Ianto nodded, he then turned around, and he opened the door and left the office slamming the door behind him. As soon as he got home, he booked a flight to San Francisco for later in the afternoon and then made a phone call to his dad and step mum that he was going to come over for a couple of weeks. They were very delighted with this news. In an hour's time he had a bag packed and leaving for the airport. He was soon sat on the plane trying to figure out the best way to tell his dad and step mum that their daughter had been murdered.

**I hope you liked this chapter please review, feedback is helpful.**


	3. Chapter 3

**Truth or lies? **

**Chapter 3**

**Note from author**

**For this chapter I want to thank fan fiction authors quiet time and PC Janto for their input on this chapter.**

**Story begins... **

As Ianto settled down in his seat, his mind began to remember things from his past.

Flashback

Seventeen year old Ianto sat in front of his father's desk, in his study, he sat opposite his father, Edgar Jones. "You want to join the marines?" Edgar asked his son he said in a very bland tone of voice.

"Yes." Ianto answered simply.

Edgar sighed, "you have outstanding grades, you can become anything you want and you want to be in the marines?"

Ianto nodded and replied, "It's what I want to do."

"Will it make you happy?" He said quietly, looking up from his reading material.

"Yes it will. I just need to get away, forget everything that happened before mum died, I believe by doing this it will help me." Ianto said smoothly.

"Go ahead and do it then, this meeting is over." Edgar said with no emotions what so ever in his voice. Ianto then just stood and walked out of the study without looking back.

Three years later- Germany base camp

Ianto and three other men were all sitting at a small table playing cards, in their sleeping quarters. Ianto looked up as the heavy door was pushed open, revealing two men in a uniform that none of the three men, including Ianto, didn't recognise. "Ianto Jones?" One of the men in uniform said in a American accent.

Ianto stood up and said "yes that's me."

"Our boss wants to see you." The man informed Ianto, "You will need to come with us." He said, he seemed to be ignoring Ianto's friends.

"Who are you?" Ianto asked with suspicion. One of the men pulled out his a small laminated piece of paper, about the size of a passport, and then handed it to Ianto. Ianto looked down at the card and read aloud "E-Corp, Specialised Black Op mission"

"Do you know who we are now Mr Jones?" The man who handed Ianto the card said in a stern voice, "you need to come with us now." He repeated. Both of the men turned, opened the door and began to walk to across the camp and Ianto quickly followed, soon catching up with them. About five minutes later they approached the bosses building. One of the men scanned their pass and entered his code into the security system; it beeped to tell that they were allowed into the building. All of them entered the building. Ianto followed the two men down the corridor until they stopped to the door on the left. The second man knocked on the door three times and opened the door, "go in." He ordered Ianto. Ianto did as he was told.

Ianto stopped dead as he saw the man at the large wooden desk, "Dad?"

End of flashback

Location: The Hub

"So Owen what have you got for me?" Jack boomed from the top of the stairs that surround and led down the medical bay.

Owen looked up and let out a sigh, "you are not going to like it Jack."

"I don't care I just want you to tell me something." Jack said his voice going back to its normal volume.

"Okay, I ran some DNA through the system and found out her name is Lily Jones." He saw the look on Jack's face, Owen then continued, "then I found out that Ianto and Lily are brother and sister. Listen Jack, maybe Ianto didn't know she was his sister, I've heard tonnes of stories where the kids mum or dad had an affair and then twenty years later the kid has a half brother or sister."

"Maybe, does Tosh know anything about Lily Jones?" Jack asked, as he turned away from Owen.

"I'm not sure Jack, knowing her she probably has a huge file on Lily." Owen joked as he watched Jack walk away towards Tosh, who was working away at the computer.

"Tosh please tell me you have something?" Jack begged when he got to her station and pulled up a chair next to her.

Tosh nodded and said "Lily Jones, brother of Ianto Jones," her breath hitched slightly but then she continued, "Lily is 24 years, two years younger than Ianto. Her father Edgar Jones, by the looks of it she wasn't exactly close with him, or her mother. I haven't been able to get any more information than that, they are other files on her but I can't seem to get into them. If I keep on trying to access them, we may be hacked because whoever is in charge of those files will know we are trying to get into them. "She explained, "I'm sorry Jack, but it's too risky." She said sadly.

"I guess that tells us that whoever she used to work for was very high in the government or not government at all, they are just like us." Jack said to Tosh.

"So who the hell are we dealing with?" Tosh breathed.

"That's a very good question." Jack sighed.

**I hoped you enjoyed this chapter, please review feedback is helpful. I'm sorry if more people msg me and I didn't get a chance to check for more, but those who did msg thank you, it was helpful. **


	4. Chapter 4

**Truth or lies?**

**Chapter 4**

Ianto finally made it to his parent's house, it took nearly half an hour to get his step mum Maria to stop crying and explain to her that it was very urgent for him to see Edgar. Maria informed Ianto that Edgar was away in New York for work. Maria had no idea that Edgar works for a top secret organisation that trains people to kill and tells them who to kill. Edgar tells her that his job is business consultant for a very high class business. Maria doesn't ask any questions as long as he brings in the money.

**Very sorry for the very short chapter, I just wanted to give you an idea what the family is like. **


	5. Chapter 5

**Truth or lies?**

**Chapter 5**

Location: Edgar and Maria Jones house- San Francisco 

"I'm sorry Ianto, but your father is away on business in New York and I would give you a contact number but I wasn't given one. He always gave one, so something must be wrong." Maria said through her un-controlled sobbing, which was driving Ianto insane.

Ianto was pacing back and forth, trying to figure out what the hell was going on. Edgar always called Ianto before going away to inform him what is happening, and he always leaves a contact number for Maria to call, so they can say good night to each other. "When was the last time you heard from him?" He asked, stopping his pacing and stood facing Maria who had finally stopped crying.

"A week ago, he called as soon as he got to the hotel in New York and that was the last time I heard from him." Maria sniffed. She asked "Ianto, what do you know?"

"Nothing, that's the problem," Ianto growled under his breath. "If you haven't heard from him in a way week, why the hell haven't you contacted the police, or why didn't you contact me?" He said angrily.

Maria let out a laugh of surprise, "you think I would call the police? I'm not stupid you know, I know what he does, and if I even try and get involved with his work they will have me killed."

Ianto stared at Maria and breathed, "You know?" Maria just nodded her reply, "how long?"

"Not that long, about six months ago I heard you and him talking about some sort of target. Then when you and your father went out I went to look in his study and found a few things, like his file and who he really was and what he does for a living. I didn't tell him I found out because I was afraid that he would kill me." Maria explained nearly close to crying again.

"I have to get to New York and find out what the hell is happening." Ianto said, hurrying over to the front door and picking up his bag which he placed there earlier when he arrived.

"Maybe I should come with you." Maria suggested, hurrying over to him.

"No you need to stay here." Ianto said simply, he then said "the company will kill you if they found out that dad is working for them." And with that Ianto left the house without even glancing back once.

Location: The Hub

Jack, Gwen, Owen and Tosh all sat at the boardroom table in silence after they all found out about the truth of Ianto and Lily Jones. "So, Ianto and that Lily girl were siblings?" Owen asked breaking the stone cold silence.

Jack looked up from his hands and looked at Owen coldly and growled "that Lily girl was Ianto's sister so show some respect."

"Sorry." Owen mumbled, hanging his head in shame.

"What is going to happen to Ianto then, when he comes back, from wherever he went?" Gwen asked suddenly.

"Nothing is going to happen to Ianto when he comes back Gwen." Jack replied simply.

"What? Jack he lied to us, we asked who she was and he said he didn't know and this isn't the first time he has lied to us either." Gwen argued.

"The only reason why he lied to us because he knew that if he told us the connection between them I would ban him from the investigation, I believe that is a good enough reason not to say anything because if any of you were in the exact same position as Ianto, you would have done the same thing." Jack practically yelled. All of them avoided Jacks gaze because they knew he was right. "So this investigation is over until Ianto gets back, we are not getting anywhere without him" He said, now a bit more softly.

"Where is Ianto exactly?" Tosh asked gently.

"I don't have a clue, I told him to go away for two weeks and I didn't ask him where he was going." Jack explained. None of them said a word, they knew not to get involved at this point. "Right" Jack said and clapped his hands, "back to work, don't you all have paperwork to do?" All of them hurried out of the boardroom, but Jack called Tosh back and then he explained to Tosh that he still wanted her to work on Lily's background.

Location: Plane- destination: New York

As Ianto was sitting in his seat he begins to remember his first ever mission with Lily.

Flashback

Location- Israel 

"I don't see why you are getting all worked up about this, it's only Russia." Lily sighed; she had all her gear laid out on the bed of the hotel room which they were staying in. For the past six months they had been training with Israeli Mousaud so they can be prepared for this mission in Moscow.

"Exactly Lily, the people who we are supposed to kill are Russian, they rats everywhere, we can't trust anyone. I don't even trust your fucking Russian source anymore, and the worst thing about the mission, it's a fucking undercover mission. We are going to be working with people whom I've never and never will trust." Ianto said, sounding exasperated.

Lily rolled her eyes, "I trust my source and I don't see the problem doing an undercover mission, we have done them before."

"It's not that I don't like undercover missions, it's just who were under covering with that's the problem." Ianto explained, he was now beginning to pack all his gear up, doing it a lot neater than Lily was doing it. Lily decided not to say anything else and continued on with her task.

**Hope you enjoyed the chapter and enjoying the story so far, please review **


	6. Chapter 6

**Truth or lies?**

**Chapter 6**

As soon as Ianto stepped out of New York airport he instantly knew something was wrong. Ianto knew at least two men were at the airport, following him and Ianto knew that it would be hard to get them off his tail. Ianto then quickly turned and entered the airport, and making his way over to the car hire desk. He then produced fake documents so that it would be harder for people to trace him, he also produced cash, due to not having a credit card not using a fake name and then he just happily smiled at the blond woman as he took the keys, knowing that he would probably never return this car in one piece.

Flashback

Ianto was seemed to be a bit happier as he learnt that the mission had changed from an undercover mission in Russia, to a undercover mission in Iraq. He still wasn't happy it being an undercover mission but in his words 'at least I never have to speak or near a Russian ever again.' Ianto and Lily were sitting in their quarters which were set up on the American Marine Military base, known as the 'Safe Zone' going over the information they had on their mission.

"Okay, by the sounds of it, it's a bitch of a mission, and we have to do it. This is the guy we have to get,' Lily said, 'Amil, he is the leader of a group who makes nuclear weapons' she slid a picture across the table to Ianto. 'We need to get inside the nuclear weapons base and extract him as quickly and as quietly as possible' Lily then showed him another picture, which was one of the nuclear bases.

"Is that it?" Ianto asked, looking up from the picture to Lily.

"That's it" Lily confirmed.

Two days later- Nuclear base

"Lily you need to get out of here!" Ianto screamed over the blaring alarm. Two of the guards had hold of Ianto and they were both waiting for a few more to come and get Lily. Ianto knew that if Lily ran now and left him behind she would be free and alive. Lily knew this and it was the only way, she stared at Ianto for a second and then ran for her life and that was the last time her and Ianto ever saw each other. The next thing Ianto knew he was being struck in the face by the butt of one of the guards guns, whicj knocked him unconscious.

Ianto then woke up a few hours later to find himself chained to a chair in the middle of a dusty room sunlit room. His head was beginning to throb from his hit. Ianto took in his surroundings. The room was large, four walls and behind him at the top of the wall was window, but Ianto knew it would be impossible to open. Ianto could feel the heat coming through the window, this then told him that it was midday. Ianto was snapped out of his thoughts as the door in front of him opened.

**Sorry to leave it like this guys. I hope you enjoyed, please review. **


	7. Chapter 7

**Truth or lies?**

**Chapter 7**

**Sorry for not writing in ages, I have been so busy with revision and coursework, it has seemed to have taken over my life. So the beginning of this chapter it carries on from when Ianto was captured and it has been three months of being on the base. This is how Ianto got hired by Torchwood 3, Lisa never happened and nor did Torchwood London. Also I think the next couple of chapters will mostly be flashbacks, and it will follow on from this one. I need to do these flashbacks so the whole story can link together in some way. Hope it works out. **

Flash back-Three months later

Ianto had been through so much pain in the past few months that he had been on the base, he had no idea how he survived. He lay there in the middle of the dark room, the only source of light was the window which as the back and right at the top and there was no way he could climb up there. The guards didn't seem to bother tying him up anymore, because they knew it was impossible for him to escape on his own.

He was on the verge of falling asleep until he heard shooting on the other side of the door. Grunting through the pain that was being caused by the bullet wound in his shoulder, and the slight throbbing from his twisted ankle. Once he managed to push himself up into a sitting position, he then pulled himself up onto his feet, but keeping more weight on his stronger leg. Ianto looked at the door as he heard movement behind, then it burst open Ianto fell back onto the floor in shock. Four people burst through the door, all pointing guns at Ianto.

All of them seemed to have a confused look on their faces. "Who the hell are you?" A tall man asked him with an American accent. But before Ianto could answer, a loud explosion caused them all to look at each other.

"We need to get out of here, what do we do with him?" The Asian women asked the tall man while gesturing towards Ianto.

The tall American man looked at Ianto for a moment and then said, "We leave and take him with us." He walked over to Ianto and offered his hand, and Ianto took it. As he was being helped he hissed as his burnt hands were touched. Jack wrapped an arm around his waist and Ianto put his arm over Jack's shoulder so he was being supported by him, which e was very glad for. "Okay, we are going to go the same way we came in, there won't be much resistance, we took out most of the guards on the way in. Tosh and Owen you go in front of us and Suzie you protect our backs. "He ordered. All of them nodded their approval.

Twenty minutes later Ianto saw light for the first time in three months and because of this he smiled for the first time for three months. He then didn't realise that he was being helped into a helicopter and sitting with complete strangers who saved his life.

**Hope you enjoyed this, please review**


	8. Chapter 8

**Truth or lies?**

**Chapter 8**

**Authors note: This chapter is a carry on from the last flashback. By the way him going to Torchwood one and Lisa did happen, I changed my mind. **

_Flashback continued_

Ianto stared at the four cups which all contained one retcon pill for each of his teammates, including Jack. That retcon pill would wipe two weeks' worth of memory that contained Ianto. He knew he had to leave, but the only way of doing that was wiping their memory, he found it easy to let got of them because he wasn't attached to them, he had only been here for two weeks. He couldn't become a field agent due to being injured and he would have to wait at least a few more weeks till was able to. He watched as all four of them took their a coffee mugs and took a sip each. He watched them began to fall asleep and as soon as he knew it was safe he left boardroom and straight to the main part of the hub.

He then went straight over to Tosh's desk and began to delete all the last two weeks of the cctv and then his file. As soon as he had done that he left not looking back.

_End of flashback_

Ianto flopped down onto the bed in his hotel room, glad that he no longer felt that someone was following him.

**Really sorry for the short chapter, just thought I should upload something**

**Please review**


	9. Chapter 9

**Truth or lies?**

**Chapter 9**

Location-Ianto's flat

Jack had been searching in Ianto's flat high and low for any indication of where Ianto was, but he couldn't find anything. Jack then slumped on the couch, tired after his search. Then he looked at the picture frame above the TV and realising that he had never thought to look behind somewhere so obvious. Jack smirked and got up and removed the frame revealing a safe in the wall. But Jack's heart sank as he soon realised how long it was going to take to open the safe. He then pulled his phone out his pocket and rang Tosh, telling her to come to Ianto's flat as soon as possible.

Half an hour later she arrived.

"Open that safe" Jack told Tosh.

Tosh sighed, realising that Jack was on a whole new level of craziness. "It's not that simple, just because I can hack into top secret files, doesn't mean I can open a safe." She explained to Jack as she was examining it. Tosh was lying, or course she could open a safe, she knew that that safe contained information that she Ianto didn't want Jack to see, and it was her mission to help Ianto, and stopping Jack from opening that safe was a way of helping him.

"Tosh?" Jack pleaded, "I need to know what is in there" He explained.

Tosh rolled her eyes and asked "why?"

"So I can find out what the bloody hell is going on!" He yelled in frustration, making Tosh jump at his sudden outburst. Even though she wanted to know what was going on, but she somehow knew that Ianto has gone for reason and it isn't her concern, it's Ianto's.

"Jack, what if he isn't here for a reason?" She gently spoke.

"What do you mean Tosh?" He asked in annoyance.

She sighed and said "I mean what if he isn't her by choice,"she paused and continued"what if he left because I wanted or had to? Maybe Torchwood was just getting too much for him and he had to get away as fast as he could, and he knew that if he told us that he was leaving we would try to stop him, and maybe not on purpose, but we would have made him feel guilty for wanting to leave a team and he probably would have stayed."

Jack didn't reply for a moment, he just sat down on the couch and then said "okay, maybe you are right, but I still need to know what is happening."

"Oh for God's sake, I am not having anymore to do with this, he left because he has his reasons, and if he ever comes back, he will decided if he wants to tell us those reasons. Yes I am sad that he has left, but it is not my business it is his. So I am going back to work, and I hope you do to." And with that Tosh left Jack sitting in shock to what she had just said.

**Sorry for the long wait, I have been so busy with exams, but I am back. So please review and tell me what you think **


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